BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 004610
(742 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 375 bits (962), Expect = e-104, Method: Compositional matrix adjust.
Identities = 192/382 (50%), Positives = 254/382 (66%), Gaps = 9/382 (2%)
Query: 360 SEDAKKYAFQRGFEIYEKMCLDEVPMNEASLTAVGRMAMSMGDGDMAFDMVKRMKSLGIN 419
+E + RGF+I+++M +D+V NEA+ T R+A++ D +MAFDMVK+MK+ GI
Sbjct: 78 TESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQ 137
Query: 420 PRLRSYGPALSVFCNNGDVDKACSVEEHMLEHGVYPEEPELEALLRVSVEAGKGDRVYYL 479
PRLRSYGPAL FC GD DKA V+ HM+E V PEEPEL ALL+VS++ D+VY
Sbjct: 138 PRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKT 197
Query: 480 LHKLRTSVRKVSPSTADVIAKWFNSKEAARLGKKKWNESLIKDTMENXXXXXXXXXXXXX 539
L +LR VR+VS ST D+I +WF S+ A + G KKW+ I+D + +
Sbjct: 198 LQRLRDLVRQVSKSTFDMIEEWFKSEVATKTGVKKWDVKKIRDAVVSGGGGWHGQGWLGT 257
Query: 540 XXXIVSHTTVGGDALCKCCGEKLAIIDLDPIETEKFAESVASIAIKRERNSSFQKFQKWL 599
V T + + +CKCC EKL ID++P+ETE FA S+ +A +RE ++F +FQ+WL
Sbjct: 258 GKWNVKRTEMDENGVCKCCKEKLVCIDINPVETETFAASLTRLACEREVKANFNQFQEWL 317
Query: 600 DYYGPFEAVVDAANVGLYSQRNFKPARVNAVVNGIRQKFPSKKWPLIVLHNRRITGHKMD 659
+ +GPF+AV+D AN+GL +QR+F ++N V +Q PSK+ PL++LH R+ G
Sbjct: 318 ERHGPFDAVIDGANMGLVNQRSFSFFQLNNTVQRCQQISPSKRLPLVILHKSRVNGGPAT 377
Query: 660 QPVNRALIEKWKNADALYATPTGSNDDCTMDNNVCFRYWLYAAIKFKCLLVTNDEMRDHT 719
P NRAL+EKWKNA ALYATP GSNDD YWLYAA+ KCLLVTNDEMRDH
Sbjct: 378 YPKNRALLEKWKNAGALYATPPGSNDDW---------YWLYAAVSCKCLLVTNDEMRDHL 428
Query: 720 FQLLGNDFFPRWKERHQVSESL 741
FQLLGN FFPRWKE+HQV S+
Sbjct: 429 FQLLGNSFFPRWKEKHQVRISV 450
Score = 78.2 bits (191), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 41/86 (47%), Positives = 56/86 (65%), Gaps = 4/86 (4%)
Query: 178 EKGSKKSKK---DRSEQFQLRVELDMCSKRGDVMGAIRLYDKAQREGIKLGQYHYNVLLY 234
E S+K+KK +S + L+ +LDMCSK+GDV+ A+RLYD+A+R G++L QYHYNVLLY
Sbjct: 10 ENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY 69
Query: 235 LCSSAAVGVVKPAKSGSGMRTLDTFE 260
+CS A G R D F+
Sbjct: 70 VCSLAEAATESSPNPGLS-RGFDIFK 94
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 356 bits (913), Expect = 3e-98, Method: Compositional matrix adjust.
Identities = 186/382 (48%), Positives = 244/382 (63%), Gaps = 9/382 (2%)
Query: 360 SEDAKKYAFQRGFEIYEKMCLDEVPMNEASLTAVGRMAMSMGDGDMAFDMVKRMKSLGIN 419
+E + RGF+I+++ +D+V NEA+ T R+A++ D + AFD VK+ K+ GI
Sbjct: 78 TESSPNPGLSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQ 137
Query: 420 PRLRSYGPALSVFCNNGDVDKACSVEEHMLEHGVYPEEPELEALLRVSVEAGKGDRVYYL 479
PRLRSYGPAL FC GD DKA V+ H +E V PEEPEL ALL+VS + D+VY
Sbjct: 138 PRLRSYGPALFGFCRKGDADKAYEVDAHXVESEVVPEEPELAALLKVSXDTKNADKVYKT 197
Query: 480 LHKLRTSVRKVSPSTADVIAKWFNSKEAARLGKKKWNESLIKDTMENXXXXXXXXXXXXX 539
L +LR VR+VS ST D I +WF S+ A + G KKW+ I+D + +
Sbjct: 198 LQRLRDLVRQVSKSTFDXIEEWFKSEVATKTGVKKWDVKKIRDAVVSGGGGWHGQGWLGT 257
Query: 540 XXXIVSHTTVGGDALCKCCGEKLAIIDLDPIETEKFAESVASIAIKRERNSSFQKFQKWL 599
V T + +CKCC EKL ID++P+ETE FA S+ +A +RE ++F +FQ+WL
Sbjct: 258 GKWNVKRTEXDENGVCKCCKEKLVCIDINPVETETFAASLTRLACEREVKANFNQFQEWL 317
Query: 600 DYYGPFEAVVDAANVGLYSQRNFKPARVNAVVNGIRQKFPSKKWPLIVLHNRRITGHKMD 659
+ +GPF+AV+D AN GL +QR+F ++N V +Q PSK+ PL++LH R+ G
Sbjct: 318 ERHGPFDAVIDGANXGLVNQRSFSFFQLNNTVQRCQQISPSKRLPLVILHKSRVNGGPAT 377
Query: 660 QPVNRALIEKWKNADALYATPTGSNDDCTMDNNVCFRYWLYAAIKFKCLLVTNDEMRDHT 719
P NRAL+EKWKNA ALYATP GSNDD YWLYAA+ KCLLVTNDE RDH
Sbjct: 378 YPKNRALLEKWKNAGALYATPPGSNDDW---------YWLYAAVSCKCLLVTNDEXRDHL 428
Query: 720 FQLLGNDFFPRWKERHQVSESL 741
FQLLGN FFPRWKE+HQV S+
Sbjct: 429 FQLLGNSFFPRWKEKHQVRISV 450
Score = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 40/86 (46%), Positives = 55/86 (63%), Gaps = 4/86 (4%)
Query: 178 EKGSKKSKK---DRSEQFQLRVELDMCSKRGDVMGAIRLYDKAQREGIKLGQYHYNVLLY 234
E S+K+KK +S + L+ +LD CSK+GDV+ A+RLYD+A+R G++L QYHYNVLLY
Sbjct: 10 ENLSRKAKKKAIQQSPEALLKQKLDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY 69
Query: 235 LCSSAAVGVVKPAKSGSGMRTLDTFE 260
+CS A G R D F+
Sbjct: 70 VCSLAEAATESSPNPGLS-RGFDIFK 94
>pdb|1S6I|A Chain A, Ca2+-Regulatory Region (Cld) From Soybean
Calcium-Dependent Protein Kinase-Alpha (Cdpk) In The
Presence Of Ca2+ And The Junction Domain (Jd)
Length = 188
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 27/91 (29%), Positives = 45/91 (49%), Gaps = 12/91 (13%)
Query: 248 KSGSGMRTLDT-------FEVSTMNSTELGDSRDMDNNGQLDYGS-SPMIDKLESNSSYR 299
K GSG TLD F + ++ ++ D DN+GQ+DYG + M+ K + N
Sbjct: 93 KDGSGYITLDEIQQACKDFGLDDIHIDDMIKEIDQDNDGQIDYGEFAAMMRKRKGNGGIG 152
Query: 300 FDDLDSTFNEKENLGQFSNGHMKLNSQLLDG 330
+ T N ++ LG NG ++Q+++G
Sbjct: 153 RRTMRKTLNLRDALGLVDNG----SNQVIEG 179
>pdb|3PYD|A Chain A, Crystal Structure Of
4-Diphosphocytidyl-2-C-Methyl-D-Erythritol Kinase (Ispe)
From Mycobacterium Tuberculosis
pdb|3PYE|A Chain A, Mycobacterium Tuberculosis
4-Diphosphocytidyl-2-C-Methyl-D-Erythritol Kinase (Ispe)
In Complex With Cdpme
pdb|3PYF|A Chain A, Mycobacterium Tuberculosis
4-Diphosphocytidyl-2-C-Methyl-D-Erythritol Kinase (Ispe)
In Complex With Amp-Pnp
pdb|3PYG|A Chain A, Mycobacterium Tuberculosis
4-Diphosphocytidyl-2-C-Methyl-D-Erythritol Kinase (Ispe)
In Complex With Adp
Length = 306
Score = 33.1 bits (74), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 407 FDMVKRMKSLGINPRLRSYGPALSVFCNNGDVDKACSVEEHMLEHGVYPEEPELEALLRV 466
++ + R++ +G PRL GP L+ GD D+ + + ++ +P L LR
Sbjct: 185 YNELDRLREVGDPPRLGEPGPVLAALA-AGDPDQLAPLLGNEMQAAAVSLDPALARALRA 243
Query: 467 SVEAGK 472
VEAG
Sbjct: 244 GVEAGA 249
>pdb|1KCX|A Chain A, X-Ray Structure Of Nysgrc Target T-45
pdb|1KCX|B Chain B, X-Ray Structure Of Nysgrc Target T-45
Length = 518
Score = 29.3 bits (64), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 18/87 (20%)
Query: 422 LRSYGPALSVFCNNGDVDKACSVEEHMLEHGVY---------PEEPELEALLRVSVEAGK 472
L+ G + V NGD+ ++ +LE G+ PEE E EA+ R AG+
Sbjct: 181 LKGLGAVILVHAENGDL--IAQEQKRILEMGITGPEGHALSRPEELEAEAVFRAIAIAGR 238
Query: 473 GDRVYYLLHKLRTSVRKVSPSTADVIA 499
+ Y+ + +S S AD+IA
Sbjct: 239 INCPVYI-------TKVMSKSAADIIA 258
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.131 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,187,462
Number of Sequences: 62578
Number of extensions: 810445
Number of successful extensions: 1641
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1632
Number of HSP's gapped (non-prelim): 9
length of query: 742
length of database: 14,973,337
effective HSP length: 106
effective length of query: 636
effective length of database: 8,340,069
effective search space: 5304283884
effective search space used: 5304283884
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)